Identification of apilimod as a first-in-class PIKfyve kinase inhibitor for treatment of B-cell non-Hodgkin lymphoma

Abstract

We identified apilimod as an antiproliferative compound by high-throughput screening of clinical-stage drugs. Apilimod exhibits exquisite specificity for phosphatidylinositol-3-phosphate 5-kinase (PIKfyve) lipid kinase and has selective cytotoxic activity in B-cell non-Hodgkin lymphoma (B-NHL) compared with normal cells. Apilimod displays nanomolar activity in vitro, and in vivo studies demonstrate single-agent efficacy as well as synergy with approved B-NHL drugs. Using biochemical and knockdown approaches, and discovery of a kinase domain mutation conferring resistance, we demonstrate that apilimod-mediated cytotoxicity is driven by PIKfyve inhibition. Furthermore, a critical role for lysosome dysfunction as a major factor contributing to apilimod's cytotoxicity is supported by a genome-wide CRISPR screen. In the screen, (master transcriptional regulator of lysosomal biogenesis) and endosomal/lysosomal genes, , and were identified as important determinants of apilimod sensitivity. These findings thus suggest that disruption of lysosomal homeostasis with apilimod represents a novel approach to treat B-NHL.

Snx10 and PIKfyve are required for lysosome formation in osteoclasts

“…In the report by Gayle et al, we noted with interest that apilimod cytotoxicity in B‐cell non‐Hodgkin lymphoma was dependent on expression of known, essential osteoclast effector mRNAs, CLCN7, OSTM1, and Snx10. We, therefore, postulated that the expression of Snx10 may determine apilimod's ability to inhibit lysosome formation in osteoclasts.…”

“…As part of our efforts to better understand the mechanisms by which Snx10 regulates osteoclast function, we took note of a recent report that tested the potential of a small molecule, apilimod, to treat non‐Hodgkin's B‐cell lymphoma (NHBL). Apilimod acts by binding the phosphoinositide(3)phosphate kinase (PI3P kinase), PIKfyve, with nanomolar specificity and inhibiting it.…”

Lysosomes as a therapeutic target

“…It was well tolerated in more than 700 human subjects (normal healthy volunteers and patients with inflammatory disease), but the clinical trials did not meet their primary endpoints and further development was abandoned. Apilimod is currently being evaluated in a clinical trial (NCT02594384) aimed at defining a maximum tolerated dose in patients with B cell non Hodgkin lymphoma and monitoring safety, pharmacokinetics, pharmacodynamics and prelimi nary efficacy 307 . YM201636 is another selective inhibi tor of PIKfyve (TABLe 4; Fig.…”

The complex relationship between TFEB transcription factor phosphorylation and subcellular localization

“…The RagD GTPase is important for an efficient mTORC1 recruitment to the lysosomal surface. In addition to promoting various cancers, TFEB was also recently identified as being highly expressed in non-Hodgkins lymphoma where it may render these cancer cells sensitive to apilimod-mediated inhibition of the PIKfyve lipid kinase (Gayle et al, 2017). Furthermore, xenotransplantation experiments performed using a melanoma cell line showed that silencing of RagD significantly reduced tumor growth (Di Malta et al, 2017).…”

“…These include infection (Visvikis et al, 2014;Campbell et al, 2015;Pastore et al, 2016), bacterial phagocytosis (Gray et al, 2016), inflammation (i.e., LPS treatment; Pastore et al, 2016), physical exercise (in muscle; Mansueto et al, 2017), mitochondrial damage (Nezich et al, 2015), PIKfyve inhibition (Gayle et al, 2017), and ER stress . These include infection (Visvikis et al, 2014;Campbell et al, 2015;Pastore et al, 2016), bacterial phagocytosis (Gray et al, 2016), inflammation (i.e., LPS treatment; Pastore et al, 2016), physical exercise (in muscle; Mansueto et al, 2017), mitochondrial damage (Nezich et al, 2015), PIKfyve inhibition (Gayle et al, 2017), and ER stress .…”